Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
VDR

Cell type

Cell type Class
Prostate
Cell type
RC43N
NA
NA

Attributes by original data submitter

Sample

source_name
RC43N
tissue
RC43N
cell line
RC43N
cell type
WT
genotype
African American non-malignant prostate
chip antibody
VDR
treatment
Vehicle

Sequenced DNA Library

library_name
GSM6900281
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Briefly, approximately 20x106 cells were crosslinked with 1% formaldehyde solution, quenched with glycine (0.125 M) and harvested in cold PBS. Sonication of crosslinked chromatin was performed using a Bioruptor® UCD-200TM Sonicator (Diagenode) with optimized cycles for each cell type. Immunoprecipitation of sonicated material was performed with antibodies against VDR (D2K6W) – Cell Signaling) or IgG (Rabbit IgG sc2729 – Santa Cruz) for 16 hours, and antibody/bead complexes isolated with Magna ChIPTM Protein A+G magnetic beads (Millipore). Complexes were washed, reverse crosslinked, and treated sequentially with RNase and proteinase K prior to DNA isolation. Sequencing libraries prepared from immunopreciptiated DNA

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
3582736
Reads aligned (%)
0.0
Duplicates removed (%)
0.5
Number of peaks
181 (qval < 1E-05)

hg19

Number of total reads
3582736
Reads aligned (%)
0.0
Duplicates removed (%)
0.6
Number of peaks
100 (qval < 1E-05)

Base call quality data from DBCLS SRA